SMTL ID : 3tm9.1

Y29A mutant of Vitreoscilla stercoraria hemoglobin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 20 residues within 4Å: Chain A: V.39, L.42, F.43, Q.53, A.56, L.57, T.60, V.61, I.81, K.84, H.85, A.88, V.90, H.94, Y.95, V.98, Y.126, I.129, A.130, F.133 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:L.42, A:F.43, A:F.43, A:A.56, A:T.60, A:I.81, A:A.88, A:V.90, A:V.90, A:Y.95, A:V.98, A:Y.126, A:F.133 Hydrogen bonds: A:Q.53 Salt bridges: A:K.84 Metal complexes: A:H.85 HEM.14: 20 residues within 4Å: Chain B: V.39, L.42, F.43, Q.53, A.56, L.57, T.60, V.61, I.81, K.84, H.85, A.88, V.90, H.94, Y.95, V.98, Y.126, I.129, A.130, F.133 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:L.42, B:F.43, B:F.43, B:A.56, B:T.60, B:I.81, B:A.88, B:V.90, B:V.90, B:Y.95, B:V.98, B:Y.126, B:F.133 Hydrogen bonds: B:Q.53 Salt bridges: B:K.84 Metal complexes: B:H.85

24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: T.23, T.26, T.27, K.30 Ligands: EDO.7 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: Q.4, N.8 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: K.79 Ligands: EDO.9 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: T.23, T.27, E.108, V.109 Ligands: EDO.4 Ligand excluded by PLIP EDO.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: P.72, L.75, P.76, K.79 Chain B: D.3, Q.4 Ligands: EDO.6 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: G.123, K.124, G.127, D.131 Ligands: EDO.12 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: M.1 Chain B: L.75, D.131, V.132, Q.135, V.136 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain A: Y.95, P.96, Y.126, G.127, A.130, D.131, I.134 Ligands: EDO.10 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: N.8, K.11 Ligand excluded by PLIP EDO.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: T.23, T.26, T.27, K.30 Ligands: EDO.20 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain B: Q.4, N.8 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain B: K.79 Ligands: EDO.22 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: T.23, T.27, E.108, V.109 Ligands: EDO.17 Ligand excluded by PLIP EDO.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: D.3, Q.4 Chain B: P.72, L.75, P.76, K.79 Ligands: EDO.19 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: G.123, K.124, G.127, D.131 Ligands: EDO.25 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: L.75, D.131, V.132, Q.135, V.136 Chain B: M.1 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain B: Y.95, P.96, Y.126, G.127, A.130, D.131, I.134 Ligands: EDO.23 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain B: N.8, K.11 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ratakonda, S. et al., Crystallographic structure determination of B10 mutants of Vitreoscilla hemoglobin: role of Tyr29 (B10) in the structure of the ligand-binding site. Acta Crystallogr.,Sect.F (2013)

Release Date

2014-04-16

Peptides

Bacterial hemoglobin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Bacterial hemoglobin